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PAM50 normalized metrics

This repository contains CSV files of spinal cord morphometric measures in the PAM50 anatomical dimensions computed from 203 healthy adult volunteers.

👉 Please cite this work if you use it or if you are inspired by it:

Valošek, Bédard et al., (2024). A database of the healthy human spinal cord morphometry in the PAM50 template space. Imaging Neuroscience, 2 1–15, https://doi.org/10.1162/imag_a_00075

DOI

👉 For interactive figures, please visit the NeuroLibre preprint:

Valošek, Bédard et al., (2023). A database of the healthy human spinal cord morphometry in the PAM50 template space. NeuroLibre Reproducible Preprints, 17, https://doi.org/10.55458/neurolibre.00017

DOI

Usage

The repository is part of SCT and is downloaded automatically during SCT installation.

CSV files from this repository are used by the following SCT functions:

  • sct_process_segmentation -normalize-PAM50 1, example:
sct_process_segmentation -i sub-001_T2w_label-SC_mask.nii.gz -vertfile sub-001_T2w_label-SC_mask_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -o sub-001_T2w_metrics_PAM50.csv
  • sct_compute_compression -normalize-hc 1, example:
sct_compute_compression -i sub-001_T2w_label-SC_mask.nii.gz -vertfile sub-001_T2w_label-SC_mask_labeled.nii.gz -l sub-001_T2w_label-compression.nii.gz -normalize-hc 1 -o sub-001_T2w_compression_metrics.csv

Dependencies

The CSV files were generated using process_data_spine-generic.sh, r20230222 script from the spine-generic/data-multi-subject, r20230223 dataset.